Aircraft: WIDEBODY; LOW WING; 2 TURBOJET ENG
Phase of flight: Taxi
Anomaly: ATC Issue All Types; Conflict Ground Conflict; Less Severe; Deviation / Discrepancy - Procedural Published Material / Policy; Deviation / Discrepancy - Procedural Clearance; Ground Incursion Runway

We were vectored for the ILS to Runway 06 by RPLL tower. During our briefing we discussed turning off at the high speed taxiway R1. During my review of the notes on page 10-9; I took note of the procedures for landing on Runway 06 while aircraft may be departing on Runway 13. Approach and landing were normal. I used Auto-brakes 3. We exited R1 at low speed; maybe 30 knots and were still slowing to normal taxi speed. Tower stated '[Aircraft X]; turn on Charlie'. With a quick glance at the taxi chart; we continued straight to turn right on Charlie taxiway. At that moment I was sure that this was the intent of the tower controller's instructions. If he had meant for us to turn left on Charlie; he would have had to tell us to first turn left on R2 and then left on Charlie. Additionally; as per 10-9; there is not supposed to be traffic on take-off from runway 13 while we were still moving. We were barely over the hold short line and the tower said '[Aircraft X]! You are on the runway!'. At that point we were NOT on the runway; but our nose was over a hold short line. I looked left and there was an aircraft airborne off runway 13 and climbing through about 50 feet. He was at least 4;000 feet from our position. Fortunately; at no time were we in danger of a catastrophic collision with this aircraft. After this the controller had us turn left on Charlie taxiway and continue taxiing. Why did this happen? Here are all the facts; as I see them. 1. Tower gave us an incorrect and incomplete instruction. 2. We had expectation bias about our next instruction. 3. We were unfamiliar with the airport. 4. We were not given adequate information from flight control about where to park. 5. This duty night is a well-documented risk to safety and service. It is one of the longest and most difficult duty periods currently being flown by the fleet. 1. The tower controllers said; '[Aircraft X]; turn on Charlie'. These were his exact words - I wrote them down when we stopped and were delayed during taxi to our parking area. No other instructions were given except those words. I was not taxiing the aircraft - but if I had been; I would have continued straight ahead as the captain did. It was the only logical way to go; having been given those instructions. We assumed that runway 13 would not be in use; as per 10-9. The fact is; the aircraft that was cleared for takeoff on runway 13 had to have been so cleared while we were on short final; which is contrary to the text on 10-9. Also; according to what I see on the airport diagram; in the hot spot blow up section; at no time were we on the runway. I think the controller said that in error. Additionally; we were not told to turn on R2; we did not know where we were going to park and we were attempting to get clear of the active runway. 2. The expectation bias really needs no explanation. We thought we were going to; and supposed to do something different from what the Tower expected. At international airports; it is expected that you get your aircraft clear of the active runway as well. 3. This was a last minute change to our schedule. We each had flown into Manila before; but it has been at least 12 years. The area where this occurred is a hot spot area. 4. We should have been given more information about why and what we were supposed to do in Manila. On the ground before takeoff we were given a flight release; Gen Decs and weather. We assumed that a load and unload would occur. I did not ask for runway data because I assumed they would give us that in Manila. We communicated with Dispatch on the way to Manila - he was very helpful and tried to get us a parking spot. All we were given was a potential parking spot; but not exactly where to go or who to contact on the ground in Manila. When we landed; we took a 28 minute taxi delay as tower had to find out where we were parking. We were also further delayed on the ground due to incomplete paperwork. Nobody told us this was just a tech stop. That information should have been conveyed to the Captain. If it had been; we would have been able to get what we needed - from who we needed it - in a more timely manner. We could have reviewed the non-maintenance staffed airport procedures; made sure we had a number or name to tell tower on the ground to avoid the taxi delay; we could have made sure that we had all the paperwork we needed and avoided the delays while talking on satcom to a Duty Manager. All that information is pertinent to the flight. It was obviously a big decision in operations about what to do with flights going to our original destination. Why wouldn't anybody inform the crews of ALL the information about what decisions were being made related to our flight? 5. I have been told that this 3 leg night has been written up in event reports and that it has generated fatigue calls by crews doing this night. This trip is well known among us to be a potentially unsafe night for the crews. We are operating at max duty; into and out of 4 different countries in the middle of the night. We contend with weather; language issues; non-standard clearances by foreign controllers and long complicated taxi instructions. Every time I have done the trip it goes past scheduled duty time. It is very hard to understand why this trip remains part of the bid package. Word from the crews that fly it is that it has been written up and discussed with the company and the union numerous times. Maybe that is not good information; or people are saying that they write it up and fatigue calls have happened; but they haven't. All I know for a fact is my experience on this trip. I am not sure why we keep this trip when it is clearly a risk to our safety and making service for our customers. Did the length of the duty day play a part in this? Absolutely. The Captain is very experienced - and I am a very senior First Officer (FO) with 13 plus years on the aircraft and years of Asia experience. I was well rested for this duty night. I planned for almost 4 days on how and when to sleep to get ready for this single night. Every time I have done this trip the Captain and I both fall asleep in the car on the way to the hotel. It's impossible to stay awake. The long hotel travel times are also a valid consideration relating to crew rest in Asia. I assume that the folks who put together this trip have not actually flown this night. It is time to reduce this duty night. It is irresponsible and dangerous to continue to schedule this pairing. We have made so many positive changes relating to safety it really is confusing to still see this pairing. It is my hope that maybe this report will spark a discussion about making a change. Pilot Monitoring (PM) on final approach for Runway 06; I asked the tower if R-1 was open; they confirmed it was open. After exiting Runway 06 at R1 tower instructed: '[Aircraft X]; turn onto taxiway C'. It appeared to me I was past R2; continued straight ahead to end of R1 and join C. Both pilots were in agreement. Tower suddenly said 'Stop; [Aircraft X]' we complied. ATC said we were on the runway; we were past hold line but definitely not on the runway. There was no Threat! Next the Tower told us to turn left C; right on J and hold on J. Tower or the crew didn't know where we were going to park. It took 20 minutes to finally get a parking spot. Prior to landing I had studied the insert on 10-9 it showed that the end of R13 ends at G3 far left of where we where I saw NO hold lines on that 10-9 insert depicted it is labeled E3. After tower told us to Stop; I looked left and saw an aircraft already airborne half way down the runway. There was NO Threat! After much discussion; thought and research of 10-9 page. I believe that the instruction from the Tower was not specific enough '[Aircraft X]; turn to join C'. It would of been clearer if they would of said; 'left R2; left on C'. MY question is why would ATC clear an aircraft for takeoff on R13 when we were not stopped or clear of R1? I believe this could of been an error on ATC part as well. Unfamiliar airport; not knowing where we were going to park prior to landing. I was focused on the 10-9 insert not looking outside at the time we crossed the hold line. During the TOD brief I missed briefing the last note which states: 'R06 vacating; take R1; R2 for C'. Long duty day scheduled by the company 13:23 actual 13:55. I was awake 3 hours prior to hotel lobby show time making it a 16:55 day for myself. During an earlier stop; rest facility NOT available in a TIMELY manner and unable to rest there; starting to feel the oncoming effects of fatigue and not making the call. All of these chains together was the cause of this crew error. I have filed Pairing Event report concerning the fatigue producing duty day; we were scheduled for by the company. The bottom line is I'm the Captain and take full responsibility of this taxi error. After landing on Runway 06 at Manila; crew exited on to Taxiway R1; but failed to continue taxiing onto R2 and left on C as stated in the airport diagram notes. As a result the aircraft crossed the Hold-Short line for the Runway 13 extension.